Error from import cell2location

Hi, I was just wondering whether anyone could interpret this error or give me any tips how to fix it? I’ve installed cell2location in a conda environment as per the instructions to do so manually but am getting this error upon trying to import it:

In [1]: import sys
   ...: import scanpy as sc
   ...: import anndata
   ...: import pandas as pd
   ...: import numpy as np
   ...: import os
   ...:
   ...: data_type = 'float32'
   ...:
   ...: import cell2location
   ...:

LoweringError: Failed in nopython mode pipeline (step: nopython mode backend)
Storing i64 to ptr of i32 ('dim'). FE type int32

File "../../../.local/lib/python3.7/site-packages/umap/layouts.py", line 52:
def rdist(x, y):
    <source elided>
    result = 0.0
    dim = x.shape[0]
    ^

During: lowering "dim = static_getitem(value=$8load_attr.2, index=0, index_var=$const10.3, fn=<built-in function getitem>)" at /home/camerongw/.local/lib/python3.7/site-packages/umap/layouts.py (52)

I’m using python-3.7.10.

[yozhikoff]

Hi camerongw!

I can’t reproduce this error, but it’s definitely something related to the numba package. Are you using the 0.53.0 version? Could you please try the following?

conda update numba

[vitkl]

I would strongly recommend using a separate conda environment for cell2location and other tools you are using.

If you are already doing that your error suggests that python uses umap from .local/lib/python3.7/site-packages/umap rather than conda environment. This is a common error in some HPC and can be solved by disabling the pip user site by adding this line to your .bashrc:

export PYTHONNOUSERSITE="canbeanyletters"

You also need to make sure that you active the conda environment, and that your $PATH environmental variable contains path to the conda environment before the path to any other python installation.